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Protein

Alpha-galacturonidase

Gene

lplD

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Alpha-galacturonidase able to catalyze the hydrolysis of the chromogenic substrate p-nitrophenyl-alpha-D-galacturonic acid (pNPalphaGalUA), and of the probable natural substrate alpha-1,4-di-galacturonate (GalUA2). Can neither hydrolyze pNPbetaGalUA, nor the stereoisomeric pNPalphaGlcUA. Does not display alpha- or beta-glucosidase activity as it fails to hydrolyze melibiose, raffinose, lactose and the chromogenic analogs, pNPalphaGal and pNPbetaGal. Cannot use the following compounds as substrates: pNP-N-acetyl-alpha- and beta-D-galactosaminide, pNP-N-acetyl-alpha- and beta-D-glucosaminide, pNP-alpha-L- and beta-L-arabinopyranoside, pNP-alpha- and beta-D-glucuronide, pNP-alpha- and beta-D-glucopyranoside, pNP-alpha- and beta-D-glucopyranoside 6-phosphate, pNP-alpha-D-galactopyranoside 6-phosphate and oNP-beta-D-galactopyranoside 6-phosphate.1 Publication

Catalytic activityi

((1->4)-alpha-D-galacturonide)(n) + H2O = ((1->4)-alpha-D-galacturonide)(n-1) + D-galacturonate.1 Publication

Cofactori

Protein has several cofactor binding sites:
  • NAD+1 Publication
  • Mn2+1 PublicationNote: Binds 1 Mn2+ ion per subunit. Although a Mg2+ ion is seen in the structure, galacturonidase activity was shown using manganese (PubMed:23416295).1 Publication

Kineticsi

kcat is 3.6 sec(-1) with pNPalphaGalUA as substrate (at about 37 degrees Celsius).

  1. KM=0.62 µM for pNPalphaGalUA (at about 37 degrees Celsius)1 Publication
  1. Vmax=4.33 µmol/min/mg enzyme with pNPalphaGalUA as substrate (at about 37 degrees Celsius)1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei151 – 1511SubstrateBy similarity
Metal bindingi173 – 1731Manganese
Active sitei174 – 1741Proton donorBy similarity
Metal bindingi210 – 2101Manganese

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi10 – 7263NADBy similarityAdd
BLAST

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Glycosidase, Hydrolase

Keywords - Biological processi

Carbohydrate metabolism

Keywords - Ligandi

Manganese, Metal-binding, NAD

Enzyme and pathway databases

BioCyciBSUB:BSU07130-MONOMER.

Protein family/group databases

CAZyiGH4. Glycoside Hydrolase Family 4.

Names & Taxonomyi

Protein namesi
Recommended name:
Alpha-galacturonidase (EC:3.2.1.67)
Gene namesi
Name:lplD
Ordered Locus Names:BSU07130
OrganismiBacillus subtilis (strain 168)
Taxonomic identifieri224308 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
Proteomesi
  • UP000001570 Componenti: Chromosome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi172 – 1721C → L: Does not significantly affect alpha-galacturonidase activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 446446Alpha-galacturonidasePRO_0000169862Add
BLAST

Proteomic databases

PaxDbiP39130.

Interactioni

Subunit structurei

Homotetramer.2 Publications

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100004003.

Structurei

Secondary structure

1
446
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi10 – 156Combined sources
Turni16 – 183Combined sources
Helixi22 – 3211Combined sources
Beta strandi38 – 436Combined sources
Helixi47 – 5711Combined sources
Beta strandi65 – 695Combined sources
Helixi73 – 775Combined sources
Beta strandi81 – 855Combined sources
Helixi92 – 1009Combined sources
Helixi101 – 1055Combined sources
Beta strandi113 – 1153Combined sources
Helixi116 – 14025Combined sources
Beta strandi144 – 1485Combined sources
Helixi153 – 16311Combined sources
Beta strandi168 – 1714Combined sources
Helixi175 – 19117Combined sources
Helixi198 – 2003Combined sources
Beta strandi201 – 2088Combined sources
Beta strandi211 – 2199Combined sources
Helixi224 – 23512Combined sources
Turni236 – 2383Combined sources
Helixi257 – 26610Combined sources
Beta strandi267 – 2704Combined sources
Helixi274 – 2774Combined sources
Helixi285 – 2873Combined sources
Turni289 – 2935Combined sources
Helixi299 – 31820Combined sources
Helixi332 – 3398Combined sources
Beta strandi345 – 3528Combined sources
Beta strandi354 – 3574Combined sources
Beta strandi364 – 37310Combined sources
Beta strandi376 – 3805Combined sources
Helixi387 – 40923Combined sources
Helixi412 – 42110Combined sources
Helixi429 – 43911Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3FEFX-ray2.20A/B/C/D7-446[»]
ProteinModelPortaliP39130.
SMRiP39130. Positions 7-440.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP39130.

Family & Domainsi

Sequence similaritiesi

Belongs to the glycosyl hydrolase 4 family.Curated

Phylogenomic databases

eggNOGiENOG4105F8D. Bacteria.
COG1486. LUCA.
HOGENOMiHOG000270081.
InParanoidiP39130.
OMAiKAIGCCH.
OrthoDBiEOG6CP3SG.
PhylomeDBiP39130.

Family and domain databases

Gene3Di3.40.50.720. 1 hit.
3.90.110.10. 1 hit.
InterProiIPR019802. GlycHydrolase_4_CS.
IPR001088. Glyco_hydro_4.
IPR022616. Glyco_hydro_4_C.
IPR015955. Lactate_DH/Glyco_Ohase_4_C.
IPR016040. NAD(P)-bd_dom.
[Graphical view]
PfamiPF02056. Glyco_hydro_4. 1 hit.
PF11975. Glyco_hydro_4C. 1 hit.
[Graphical view]
PRINTSiPR00732. GLHYDRLASE4.
SUPFAMiSSF51735. SSF51735. 1 hit.
SSF56327. SSF56327. 1 hit.
PROSITEiPS01324. GLYCOSYL_HYDROL_F4. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P39130-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MFHISTLDQI KIAYIGGGSQ GWARSLMSDL SIDERMSGTV ALYDLDFEAA
60 70 80 90 100
QKNEVIGNHS GNGRWRYEAV STLKKALSAA DIVIISILPG SLDDMEVDVH
110 120 130 140 150
LPERCGIYQS VGDTVGPGGI IRGLRAVPIF AEIARAIRDY APESWVINYT
160 170 180 190 200
NPMSVCTRVL YKVFPGIKAI GCCHEVFGTQ KLLAEMVTER LGIEVPRRED
210 220 230 240 250
IRVNVLGINH FTWITKASYR HIDLLPIFRE FSAHYGESGY ELEGECWRDS
260 270 280 290 300
VFCSAHRVAF DLFETYGAIP AAGDRHLAEF LPGPYLKQPE VWKFHLTPIS
310 320 330 340 350
FRKQDRAEKR QETERLIVQQ RGVAEKASGE EGVNIIAALL GLGELVTNVN
360 370 380 390 400
MPNQGQVLNL PIQAIVETNA FITRNRVQPI LSGALPKGVE MLAARHISNQ
410 420 430 440
EAVADAGLTK DTGLAFQAFL NDPLVQIDRS DAEQLFNDML QCIMQS
Length:446
Mass (Da):49,487
Last modified:December 15, 1998 - v2
Checksum:i691FEC5C371B9F5B
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti66 – 661R → T in AAA22577 (Ref. 1) Curated
Sequence conflicti154 – 1541S → Y in AAA22577 (Ref. 1) Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L19165 Genomic DNA. Translation: AAA22577.1.
AL009126 Genomic DNA. Translation: CAB12532.1.
PIRiC69653.
RefSeqiNP_388594.1. NC_000964.3.
WP_003244472.1. NZ_JNCM01000032.1.

Genome annotation databases

EnsemblBacteriaiCAB12532; CAB12532; BSU07130.
GeneIDi938770.
KEGGibsu:BSU07130.
PATRICi18973074. VBIBacSub10457_0751.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L19165 Genomic DNA. Translation: AAA22577.1.
AL009126 Genomic DNA. Translation: CAB12532.1.
PIRiC69653.
RefSeqiNP_388594.1. NC_000964.3.
WP_003244472.1. NZ_JNCM01000032.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3FEFX-ray2.20A/B/C/D7-446[»]
ProteinModelPortaliP39130.
SMRiP39130. Positions 7-440.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100004003.

Protein family/group databases

CAZyiGH4. Glycoside Hydrolase Family 4.

Proteomic databases

PaxDbiP39130.

Protocols and materials databases

DNASUi938770.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB12532; CAB12532; BSU07130.
GeneIDi938770.
KEGGibsu:BSU07130.
PATRICi18973074. VBIBacSub10457_0751.

Phylogenomic databases

eggNOGiENOG4105F8D. Bacteria.
COG1486. LUCA.
HOGENOMiHOG000270081.
InParanoidiP39130.
OMAiKAIGCCH.
OrthoDBiEOG6CP3SG.
PhylomeDBiP39130.

Enzyme and pathway databases

BioCyciBSUB:BSU07130-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP39130.

Family and domain databases

Gene3Di3.40.50.720. 1 hit.
3.90.110.10. 1 hit.
InterProiIPR019802. GlycHydrolase_4_CS.
IPR001088. Glyco_hydro_4.
IPR022616. Glyco_hydro_4_C.
IPR015955. Lactate_DH/Glyco_Ohase_4_C.
IPR016040. NAD(P)-bd_dom.
[Graphical view]
PfamiPF02056. Glyco_hydro_4. 1 hit.
PF11975. Glyco_hydro_4C. 1 hit.
[Graphical view]
PRINTSiPR00732. GLHYDRLASE4.
SUPFAMiSSF51735. SSF51735. 1 hit.
SSF56327. SSF56327. 1 hit.
PROSITEiPS01324. GLYCOSYL_HYDROL_F4. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The complete lpl cluster of Bacillus subtilis."
    Gomez A., Ramon D., Sanz P.
    Submitted (JAN-1994) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: 168 / Marburg / ATCC 6051 / DSM 10 / JCM 1465 / NBRC 13719 / NCIMB 3610 / VKM B-501.
  2. "The complete genome sequence of the Gram-positive bacterium Bacillus subtilis."
    Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S., Bruschi C.V.
    , Caldwell B., Capuano V., Carter N.M., Choi S.-K., Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F., Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D., Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M., Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P., Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K., Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S., Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y., Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G., Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J., Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C., Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S., Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B., Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S., Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M., Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y., Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J., Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A., Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M., Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S., Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E., Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K., Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E., Yoshikawa H., Danchin A.
    Nature 390:249-256(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 168.
  3. "alpha-Galacturonidase(s): A new class of Family 4 glycoside hydrolases with strict specificity and a unique CHEV active site motif."
    Thompson J., Pikis A., Rich J., Hall B.G., Withers S.G.
    FEBS Lett. 587:799-803(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, COFACTOR, KINETIC PARAMETERS, SUBUNIT, MUTAGENESIS OF CYS-172.
    Strain: 168.
  4. "Crystal structure of putative glucosidase LplD from Bacillus subtilis."
    New York SGX Research Center for Structural Genomics (NYSGXRC)
    Submitted (DEC-2008) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (2.20 ANGSTROMS) OF 7-446 IN COMPLEX WITH MAGNESIUM, SUBUNIT.

Entry informationi

Entry nameiLPLD_BACSU
AccessioniPrimary (citable) accession number: P39130
Secondary accession number(s): O31532
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: December 15, 1998
Last modified: June 8, 2016
This is version 115 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Bacillus subtilis
    Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
  2. Glycosyl hydrolases
    Classification of glycosyl hydrolase families and list of entries
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.